Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
276
datasets available to search
ShareScore release 0.9.0
Dataset results
276 results for “Gene drive”
Coevolving plasmids drive gene flow and genome plasticity in host-associated intracellular bacteria
<p>Comparative genomics and modeling of plasmids of the obligate host-associated intracellular phylum chlamydiae. </p>
Gene drives for vertebrate pest control: realistic spatial modelling of eradication probabilities and times for island mouse populations
<p>Invasive alien species continue to threaten global biodiversity. CRISPR-based gene drives, which can theoretically spread through populations despite imparting a fitness cost, could be used to suppress or eradicate pest populations. We develop an individual-based, spatially explicit, stochastic model to simulate the ability of CRISPR-based homing and X-chromosome shredding drives to eradicate populations of invasive mice (Mus muculus) from islands. Using the model, we explore the interactive effect of the efficiency of the drive constructs and the spatial ecology of the target population on the outcome of a gene-drive release. We also consider the impact of polyandrous mating and sperm competition, which could compromise the efficacy of some gene-drive strategies. Our results show that both drive strategies could be used to eradicate large populations of mice. Whereas parameters related to drive efficiency and demography strongly influence drive performance, we find that sperm competition following polyandrous mating is unlikely to impact the outcome of an eradication effort substantially. Assumptions regarding the spatial ecology of mice influenced the probability of and time required for eradication, with short-range dispersal capabilities and limited mate-search areas producing `chase' dynamics across the island characterised by cycles of local extinction and recolonization by mice. We also show that highly efficient drives are not always optimal, when dispersal capabilities are low, rapid local population supression around the introduction sites can cause loss of the gene drive before it can spread to the entire island. We conclude that, although the design of efficient gene drives is undoubtedly critical, accurate data on the spatial ecology of target species is critical for predicting the result of a gene-drive release.</p>
Incorporating ecology into gene drive modeling
<p>Gene drive technology, in which fast-spreading engineered drive alleles are introduced into wild populations, represents a promising new tool in the fight against vector-borne diseases, agricultural pests, and invasive species. Due to the risks involved, gene drives have so far only been tested in laboratory settings while their population-level behavior is mainly studied using mathematical and computational models. The spread of a gene drive is a rapid evolutionary process that occurs over timescales similar to many ecological processes. This can potentially generate strong eco-evolutionary feedback that could profoundly affect the dynamics and outcome of a gene drive release. We therefore argue for the importance of incorporating ecological features into gene drive models. We describe the key ecological features that could affect gene drive behavior, such as population structure, life-history, environmental variation, and mode of selection. We review previous gene drive modeling efforts and identify areas where further research is needed. As gene drive technology approaches the level of field experimentation, it is crucial to evaluate gene drive dynamics, potential outcomes, and risks realistically by including ecological processes. </p>
Data from: Gene network topology drives the mutational landscape of gene expression
Open the record for dataset details and reuse information.
Incorporating ecology into gene drive modeling
Open the record for dataset details and reuse information.
Gene drives for vertebrate pest control: realistic spatial modelling of eradication probabilities and times for island mouse populations
Open the record for dataset details and reuse information.
Data for: The 3-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence
Open the record for dataset details and reuse information.
Data from: A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo: possible implications for disease management
Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002-2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.
The Enterprise, a massive transposon carrying Spok meiotic drive genes
<p>The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Most TEs studied to date are relatively small (50 – 12000 bp), but can contribute to very large proportions of genomes. Here we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, <em>Enterprise</em>, from the model fungus <em>Podospora anserina</em>. Previously, we described a large genomic feature called the <em>Spok</em> block which is notable due to the presence of meiotic drive genes of the <em>Spok</em> gene family. The <em>Spok</em> block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within <em>P. anserina</em>, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the <em>Spok</em> block is not only capable of meiotic drive, but is also capable of transposition. More precisely, the <em>Spok</em> block represents a unique case where the <em>Enterprise</em> has captured the <em>Spoks</em>, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that <em>Enterprise</em> (without the <em>Spoks</em>) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in <em>Podospora</em>, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.</p>
Simulation models from: Can CRISPR-mediated gene drive work in pest and beneficial haplodiploid species?
<p>Gene drives based on CRISPR/Cas9 have the potential to reduce the enormous harm inflicted by crop pests and insect vectors of human disease, as well as to bolster valued species. In contrast with extensive empirical and theoretical studies in diploid organisms, little is known about CRISPR gene drive in haplodiploids, despite their immense global impacts as pollinators, pests, natural enemies of pests, and invasive species in native habitats. Here we analyze mathematical models demonstrating that, in principle, CRISPR homing gene drive can work in haplodiploids, as well as at sex-linked loci in diploids. However, relative to diploids, conditions favoring the spread of alleles deleterious to haplodiploid pests by CRISPR gene drive are narrower, the spread is slower, and resistance to the drive evolves faster. By contrast, the spread of alleles that impose little fitness cost or boost fitness was not greatly hindered in haplodiploids relative to diploids. Therefore, altering traits to minimize damage caused by harmful haplodiploids, such as interfering with transmission of plant pathogens, may be more likely to succeed than control efforts based on introducing traits that reduce pest fitness. Enhancing fitness of beneficial haplodiploids with CRISPR gene drive is also promising.</p>
Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes
<p>Active electroreception — the ability to detect objects and communicate with conspecifics via the detection and generation of electric organ discharges (EODs) — has evolved convergently in several fish lineages. South American electric fishes (Gymnotiformes) are a highly species-rich group, possibly in part due to evolution of an electric organ (EO) that produces diverse EODs. Neofunctionalization of a voltage-gated sodium channel accompanied the evolution of electrogenic tissue from muscle and resulted in a novel gene (scn4aa) uniquely expressed in the EO. Here, we investigate the link between variation in scn4aa and differences in EOD waveform. We combine gymnotiform scn4aa sequences encoding the C-terminus of the Nav1.4a protein with biogeographic data and EOD recordings. We test whether physiological transitions among EOD types accompany differential selection pressures on scn4aa. We found positive selection on scn4aa coincided with shifts in EOD types. Species that evolved in the absence of predators, which likely selected for reduced EOD complexity, exhibited increased scn4aa evolutionary rates. We model mutations in the protein that may underlie changes in protein function and discuss our findings in the context of gymnotiform signalling ecology. Together, this work sheds light on the selective forces underpinning major evolutionary transitions in electric signal production.</p>
Genetic and transcriptomic datasets characterizing gene drive mosquitoes expressing antimicrobial peptides that retard Plasmodium sporogonic development
<p><span>Gene drives hold promise for the genetic control of malaria vectors. The development of vector population modification strategies hinges on the availability of effector mechanisms impeding parasite development in transgenic mosquitoes. We augmented a midgut gene of the malaria mosquito <em>Anopheles gambiae</em> to secrete two exogenous antimicrobial peptides, Magainin 2 and Melittin. This small genetic modification, capable of efficient non-autonomous gene</span> drive, hampers oocyst development in both <em>Plasmodium falciparum</em> and <em>Plasmodium berghei</em>. It delays the release of infectious sporozoites while it simultaneously reduces the lifespan <span>of homozygous female transgenic mosquitoes. Modeling the spread of this modification using a large-scale agent-based model of malaria epidemiology reveals that it can break the cycle of disease transmission across a range of transmission intensities.</span></p>
Supplementary Dataset for the paper "Population suppression with dominant female-lethal alleles is boosted by homing gene drive"
<p>Supplementary Dataset for the paper "Population suppression with dominant female-lethal alleles is boosted by homing gene drive"</p>
Mating preferences can drive expansion or contraction of MHC gene family
MHC-based mating rules can evolve as a way to avoid inbreeding or to increase offspring immune competence. While the role of mating preference in the MHC diversity in vertebrates has been acknowledged, its impact on individual MHC diversity has not been considered. Here, we use computer simulations to investigate how simple mating rules favouring MHC-dissimilar partners affect the evolution of the number of MHC variants in individual genomes, accompanying selection for resistance to parasites. We showed that the effect of such preferences could sometimes be dramatic. If preferences are aimed at avoiding identical alleles, e.g. under strong selection against sib-mating, the equilibrium number of MHC alleles is much smaller than under random mating. However, if the mating rule minimises the ratio of shared to different alleles in partners, MHC number is higher than under random mating. Additionally, our simulations revealed that a negative correlation between the numbers of MHC variants in mated individuals can arise from simple rules of MHC-disassortative mating. Our results reveal unexpected potential of MHC-based mating preferences to drive MHC gene family expansions or contractions and highlight the need to study the mechanistic basis of such preferences.
Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and non-target Drosophila species
<p><span>Genetically engineered gene drives (geGD) are potentially powerful tools for suppressing or even eradicating populations of pest insects. Before living geGD insects can be released into the environment, they must pass an environmental risk assessment (ERA) to ensure that their release will not harm valued and protected entities of the environment. A key research question concerns the likelihood that non-target species will acquire the functional GD elements; such acquisition could lead to the loss of those species and to a disruption of the ecosystem services they provide. The main route for gene flow is through hybridization between the GD insect strain and closely related species that co-occur in the area of release. Using the invasive spotted-wing drosophila, <em>Drosophila</em> <em>suzukii</em>, as a case study, we demonstrate how a combination of interspecific hybridization experiments, behavioral observations, and molecular genetic analyses can be used to assess the potential for hybridization.</span></p>
Male dispersal drives gene flow in Timber Rattlesnakes (Crotalus horridus)
<p class="MsoNormal">Threatened across much of their range, timber rattlesnakes (<em>Crotalus horridus</em>) exhibit patterns in movement and genetic diversity that are shaped by many aspects of their environments in ways that may foster or constrain conservation. We combine movement data with nuclear and mitochondrial population genetic data to understand the population structure of snakes in four overwintering sites (hibernacula) in central Pennsylvania. Our analyses support the conclusion that hibernacula separated by only a few kilometers can represent genetically distinct populations. In addition, as the first dataset to compare nuclear and mitochondrial patterns in<em> C. horridus</em>, we provide novel evidence for how likely asymmetry in gene flow (with males responsible for inter-hibernaculum matings) shapes timber rattlesnake population genetics.</p>
Data for: Plio-Pleistocene climatic fluctuations and divergence with gene flow drive continent-wide diversification in an African bird
Open the record for dataset details and reuse information.
The Enterprise, a massive transposon carrying Spok meiotic drive genes
Open the record for dataset details and reuse information.
Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes
Open the record for dataset details and reuse information.
Development and testing of a novel Killer-Rescue self-limiting gene drive system in Drosophila melanogaster
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.